Analysis of short tandem repeats (STRs) of individual human genomes is routinely used, e.g., in human identity testing, and in testing of other organisms. STRs are simple sequence motifs of a few up to several dozen repeat units. Thousands of STRs can be found in the human genome. Since STRs are polymorphic with respect to their number of repeat units, individuals such as human individuals can be distinguished from each other by the unique number of repeat units per allele and per STR region or locus. Therefore, the analysis of STRs is especially useful for identifying human individuals, e.g., in forensic science or parental testing.
The United States Federal Bureau of Investigation (FBI) has established and maintains a Combined DNA Index System (CODIS), a database of STR typing information. Local, state, and national law enforcement agencies use the CODIS system to match forensic DNA evidence collected at crime scenes with STR information in the database. CODIS and other international database systems such as the European Standard Set have proven to be an effective tool for use in solving crimes and identifying individuals.
Generally, analysis of STR regions involves the isolation of genomic DNA of a human individual, followed by a polymerase chain reaction (PCR) amplification step to enrich the nucleic acid sequence containing the target STR regions. After the amplification step of selected genomic fragments, the length of each amplified STR allele is determined using, e.g., capillary electrophoresis, and compared to a standardized allelic ladder. Other methods for determining the length of each amplified STR include hybridization techniques and in some cases, capture and/or reporter probes. Additional techniques for identifying the target STR allele(s) include kinetic measurements of the amplified STR, e.g., melting temperature analysis or mass measurements, e.g., mass spectrometry such as time-of-flight mass spectrometry (MALDI-TOF-MS).
The alleles at a single STR locus may be the same for two different individuals in a population, especially if the individuals are genetically related. The probability that the alleles of two individuals will be identical at several different STR loci decreases as the number of examined loci increases. If a sufficient number of loci are examined, an overall STR allelic pattern that is unique of each individual emerges. Therefore, it is possible to establish with scientific certainty whether or not a DNA sample has originated from a particular individual. As such, an individual's unique pattern of STR alleles can be used as a DNA fingerprint.